CDC and NCBI Coordinate Wastewater-based Genomic Surveillance Data
by Mia Catharine Mattioli , PhD , National Wastewater Surveillance System , Waterborne Disease Prevention Branch , Centers for Disease Control and Prevention and Ilene Karsch Mizrachi , PhD , Intramural Research Program , Information Engineering Branch , National Center for Biotechnology Information , National Library of Medicine , National Institutes of Health .
Benefits of Wastewater Sequencing
Since wastewater is essentially a pooled community sample , one of the most promising applications of wastewater surveillance is community-level variant tracking . Variant tracking in wastewater is currently done using two different approaches : by targeting known mutations through reverse transcriptase polymerase chain reaction-based
Coordinating Wastewater Sequencing Data Submission
In response to the COVID-19 pandemic , NCBI streamlined SARS-CoV-2 genome sequence submission processes to GenBank ®
and the Sequence Read Archive publicly available
, which allows for increased global coordination of SARS-CoV-2 wastewater data .
For wastewater surveillance data , CDC
and NCBI collaborated to develop a BioSample package specific for wastewater samples sequenced
for disease surveillance . The goal of this standardized data submission process was to : 1 . Create a centralized , internationally available repository of wastewaterderived pathogen genomic data for disease surveillance .
2 . Standardize wastewater metadata and ensure it is consistent with other clinical and environmental sequence databases globally . 1
Metadata for Wastewater Surveillance BioSample package
• Collection date
• Wastewater sample matrix ** and collection methods
• Population represented by the wastewater sample
• Wastewater surveillance target .
** Defined as the wastewater matrix that was sampled . Response options include raw wastewater , sewer pipeline sediments , post grit removal , primary sludge , primary effluent , secondary sludge , secondary effluent , other , restricted access , not applicable , not collected , not provided and / or missing .
Suggested but optional
• Sequencing purpose
• Sampling site total daily flow , and
• Levels of human fecal content in the sample .
12 LAB MATTERS Summer 2021